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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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Scaffold and WhatsHap (physical and statistical phasing?) #71

Open olekto opened 2 years ago

olekto commented 2 years ago

Hi, this question might be easily answered, but I've not been able to figure it out based on the documentation and the issues here.

We have an individual bird where we have Hi-C, PacBio and 10X data that will likely let us get chromsome length phasing with WhatsHap and HapCUT2 (is this what is called physical phasing?). In addition we have a number (about 50) individuals that has been RAD-sequenced where we want to phase the SNPs. If we only had the second, just running shapeit4 on the VCF from calling those SNPs would be straight forward. How can we include the physical phasing here? Can we include it as a scaffold.bcf? Or is there another way to utilise that information? Would it be beneficial at all to include that data?

Thank you for any answer you can give me.

Sincerely, Ole

odelaneau commented 2 years ago

Hi,

You need to specify the WhatsHap output as phase sets in the SHAPEIT4 VCF input file. See point 13 of the documentation.

Hope this helps,

Olivier